sci-biology:velvet-1.2.10:20160815-014831.log

sci-biology:velvet-1.2.10:20160815-014831.log (text/plain), 3.62 KB, created by Toralf Förster on 2016-08-15 07:19:44 UTC

 * Package:    sci-biology/velvet-1.2.10
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking velvet_1.2.10.tgz to /var/tmp/portage/sci-biology/velvet-1.2.10/work
>>> Source unpacked in /var/tmp/portage/sci-biology/velvet-1.2.10/work
>>> Preparing source in /var/tmp/portage/sci-biology/velvet-1.2.10/work/velvet_1.2.10 ...
 * Upstream recommendes using -O3 in CFLAGS

 * To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,
 * please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your
 * environment or /etc/make.conf, then re-emerge the package. For example:
 *   VELVET_MAXKMERLENGTH=NN emerge [options] velvet
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/velvet-1.2.10/work/velvet_1.2.10 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/velvet-1.2.10/work/velvet_1.2.10 ...
make -j1 -j1 CC=x86_64-pc-linux-gnu-gcc 'CFLAGS=-march=native -O2 -pipe -fPIC -fopenmp' 'OPT=-march=native -O2 -pipe -fPIC -fopenmp' 
rm obj/*.o obj/dbg/*.o 
rm: cannot remove 'obj/*.o': No such file or directory
rm: cannot remove 'obj/dbg/*.o': No such file or directory
make: [Makefile:51: cleanobj] Error 1 (ignored)
mkdir -p obj
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -fPIC -fopenmp -march=native -O2 -pipe -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o 
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -fPIC -fopenmp -march=native -O2 -pipe -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o 
In file included from src/run.h:34:0,
                 from src/run.c:31:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^
x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -fPIC -fopenmp -march=native -O2 -pipe -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o 
src/splay.c:25:17: fatal error: omp.h: No such file or directory
compilation terminated.
make: *** [Makefile:110: obj/splay.o] Error 1
 * ERROR: sci-biology/velvet-1.2.10::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/velvet-1.2.10::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/velvet-1.2.10::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:velvet-1.2.10:20160815-014831.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/velvet-1.2.10/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/velvet-1.2.10/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/velvet-1.2.10/work/velvet_1.2.10'
 * S: '/var/tmp/portage/sci-biology/velvet-1.2.10/work/velvet_1.2.10'